Experimental evidence proves the inadequacy of widely accepted explanations, according to collaborators at the Technical University of Munich (TUM), Ludwig-Maximilians-Universität München (LMU), and the Max Planck Institute for the Physics of Complex Systems (MPI-PKS). Living matter, which consists largely of diverse polymeric structures assembled from various types of subunits, often exhibits striking behaviors, such as a capacity for self-organization and active motion. Physicists are interested in teasing out the elementary mechanisms that underlie the "self-organized" formation of such ordered structures and collective motions. Prof. Andreas Bausch and Dr. Ryo Suzuki of TUM, Prof. Erwin Frey of LMU, and Dr. Christoph Weber of MPI-PKS report progress toward this goal. Nanoscale filaments, made up of subunits of the protein actin, form the basis of the experimental model system they are investigating. Two papers, in the journals Nature Physics and the Proceedings of the National Academy of Sciences (PNAS), present their latest results. 
A model system based on actin filaments is yielding insights into "flocking" or "swarming" behavior on the biomolecular level. (Image: Bausch & Suzuki / TUM) Experiments disprove popular theory In their experiments the researchers first immobilize motor proteins by fixing them to a glass slide. When actin filaments are added, together with a source of biochemical energy, they interact with the motors and exhibit active gliding motions. Moreover, individual filaments were found to locally adopt strongly curved configurations. The team analyzed their statistics to understand what happens when filaments collide and under what conditions interacting filaments align themselves in collective, streaming motions. In living organisms, actin microfilaments are involved in the active migration of nucleated cells and in intracellular transport processes. According to the most popular theory, the fact that thin actin filaments bend as they are propelled by motor proteins is attributable to random thermal fluctuations, i.e., Brownian motion. But this assumption is false, says Christoph Weber, first author of the PNAS paper. Brownian motion has only a very weak impact on the form of the filaments. The researchers found that the molecular motors are not only responsible for propelling the fibers, but also for causing them to form strong bends. "The filaments exhibit a range of local curvatures, the statistical distribution of which is incompatible with thermally driven motion," explains Ryo Suzuki, first author of the paper in Nature Physics. Two by two won't do In addition, the assumption that the interactions in the system are always binary in nature is not sufficient to explain the fact that, at high densities, filaments can align with each other and begin to display directed, collective motions. In fact, simultaneous encounters involving multiple agents appear to be required to account for the emergence of such collective motion. In this case, the filaments, each of which is composed of multiple subunits, apparently remain in stable alignment with each other and interact not only pairwise, but also with many other partners. The scientists observed that, depending on the density and the mean length of the filaments, a phase transition occurs in which a state of non-directed movements is abruptly transformed into one characterized by collective motions ("swarm formation"). This transition resembles the condensation of a gas into the liquid state, except that in this case, it is not the pattern of microscopic molecular motions that changes but the orientation of the molecules in the system. From a theoretical point of view, this strengthens the argument that the currently favored model for the motions of actively driven particles, which is based on the kinetic theory of gases, cannot adequately account for the behavior of such systems. Instead, it appears as if the filaments themselves act in a coordinated fashion, like molecules in a fluid state. "To understand how collective motion arises in these systems, we need to develop new theoretical concepts which go beyond the assumptions of the kinetic theory of gases," says LMU Prof. Erwin Frey. Exactly what happens at the microscopic level when filaments come into alignment, i.e., how their subunits interact with neighbors or exchange places, is not yet clear. "A better understanding of the physics of active systems," says TUM Prof. Andreas Bausch, "opens the way to determining the basic mechanisms leading to structures and patterns enabling life, and could permit scientists to construct entirely novel nanosystems based on collective behaviors." Publications Ryo Suzuki, Christoph A. Weber, Erwin Frey and Andreas R. Bausch: Polar pattern formation in driven filament systems requires non-binary particle collisions. 2015. Christoph A. Weber, Ryo Suzuki, Volker Schaller, Igor S. Aranson, Andreas R. Bausch, and Erwin Frey: Random bursts determine dynamics of active filaments. 2015.
read more "Probing pattern formation and dynamics of nanoscale 'swarms'"
A model system based on actin filaments is yielding insights into "flocking" or "swarming" behavior on the biomolecular level. (Image: Bausch & Suzuki / TUM) Experiments disprove popular theory In their experiments the researchers first immobilize motor proteins by fixing them to a glass slide. When actin filaments are added, together with a source of biochemical energy, they interact with the motors and exhibit active gliding motions. Moreover, individual filaments were found to locally adopt strongly curved configurations. The team analyzed their statistics to understand what happens when filaments collide and under what conditions interacting filaments align themselves in collective, streaming motions. In living organisms, actin microfilaments are involved in the active migration of nucleated cells and in intracellular transport processes. According to the most popular theory, the fact that thin actin filaments bend as they are propelled by motor proteins is attributable to random thermal fluctuations, i.e., Brownian motion. But this assumption is false, says Christoph Weber, first author of the PNAS paper. Brownian motion has only a very weak impact on the form of the filaments. The researchers found that the molecular motors are not only responsible for propelling the fibers, but also for causing them to form strong bends. "The filaments exhibit a range of local curvatures, the statistical distribution of which is incompatible with thermally driven motion," explains Ryo Suzuki, first author of the paper in Nature Physics. Two by two won't do In addition, the assumption that the interactions in the system are always binary in nature is not sufficient to explain the fact that, at high densities, filaments can align with each other and begin to display directed, collective motions. In fact, simultaneous encounters involving multiple agents appear to be required to account for the emergence of such collective motion. In this case, the filaments, each of which is composed of multiple subunits, apparently remain in stable alignment with each other and interact not only pairwise, but also with many other partners. The scientists observed that, depending on the density and the mean length of the filaments, a phase transition occurs in which a state of non-directed movements is abruptly transformed into one characterized by collective motions ("swarm formation"). This transition resembles the condensation of a gas into the liquid state, except that in this case, it is not the pattern of microscopic molecular motions that changes but the orientation of the molecules in the system. From a theoretical point of view, this strengthens the argument that the currently favored model for the motions of actively driven particles, which is based on the kinetic theory of gases, cannot adequately account for the behavior of such systems. Instead, it appears as if the filaments themselves act in a coordinated fashion, like molecules in a fluid state. "To understand how collective motion arises in these systems, we need to develop new theoretical concepts which go beyond the assumptions of the kinetic theory of gases," says LMU Prof. Erwin Frey. Exactly what happens at the microscopic level when filaments come into alignment, i.e., how their subunits interact with neighbors or exchange places, is not yet clear. "A better understanding of the physics of active systems," says TUM Prof. Andreas Bausch, "opens the way to determining the basic mechanisms leading to structures and patterns enabling life, and could permit scientists to construct entirely novel nanosystems based on collective behaviors." Publications Ryo Suzuki, Christoph A. Weber, Erwin Frey and Andreas R. Bausch: Polar pattern formation in driven filament systems requires non-binary particle collisions. 2015. Christoph A. Weber, Ryo Suzuki, Volker Schaller, Igor S. Aranson, Andreas R. Bausch, and Erwin Frey: Random bursts determine dynamics of active filaments. 2015.
Artificial photosynthesis used to produce renewable molecular hydrogen for synthesizing carbon dioxide into methane. Yang, who also holds appointments with UC Berkeley and the Kavli Energy NanoScience Institute (Kavli-ENSI) at Berkeley, is one of three corresponding authors of a paper describing this research in the . The paper is titled “A hybrid bioinorganic approach to solar-to-chemical conversion”. The other corresponding authors are Michelle Chang and Christopher Chang. Both also hold joint appointments with Berkeley Lab and UC Berkeley. In addition, Chris Chang is a Howard Hughes Medical Institute (HHMI) investigator. (See below for a full list of the paper’s authors.) Photosynthesis is the process by which nature harvests the energy in sunlight and uses it to synthesize carbohydrates from carbon dioxide and water. Carbohyrates are biomolecules that store the chemical energy used by living cells. In the original hybrid artificial photosynthesis system developed by the Berkeley Lab team, an array of silicon and titanium oxide nanowires collected solar energy and delivered electrons to microbes which used them to reduce carbon dioxide into a variety of value-added chemical products. In the new system, solar energy is used to split the water molecule into molecular oxygen and hydrogen. The hydrogen is then transported to microbes that use it to reduce carbon dioxide into one specific chemical product, methane. “In our latest work, we’ve demonstrated two key advances,” says Chris Chang. “First, our use of renewable hydrogen for carbon dioxide fixation opens up the possibility of using hydrogen that comes from any sustainable energy source, including wind, hydrothermal and nuclear. Second, having demonstrated one promising organism for using renewable hydrogen, we can now, through synthetic biology, expand to other organisms and other value-added chemical products.” The concept in the two studies is essentially the same - a membrane of semiconductor nanowires that can harness solar energy is populated with bacterium that can feed off this energy and use it to produce a targeted carbon-based chemical. In the new study, the membrane consisted of indium phosphide photocathodes and titanium dioxide photoanodes. Whereas in the first study, the team worked with Sporomusa ovata, an anaerobic bacterium that readily accepts electrons from the surrounding environment to reduce carbon dioxide, in the new study the team populated the membrane with Methanosarcina barkeri, an anaerobic archaeon that reduces carbon dioxide using hydrogen rather than electrons. “Using hydrogen as the energy carrier rather than electrons makes for a much more efficient process as molecular hydrogen, through its chemical bonds, has a much higher density for storing and transporting energy,” says Michelle Chang. In the newest membrane reported by the Berkeley team, solar energy is absorbed and used to generate hydrogen from water via the hydrogen evolution reaction (HER). The HER is catalyzed by earth-abundant nickel sulfide nanoparticles that operate effectively under biologically compatible conditions. Hydrogen produced in the HER is directly utilized by the Methanosarcina barkeri archaeons in the membrane to produce methane. “We selected methane as an initial target owing to the ease of product separation, the potential for integration into existing infrastructures for the delivery and use of natural gas, and the fact that direct conversion of carbon dioxide to methane with synthetic catalysts has proven to be a formidable challenge,” says Chris Chang. “Since we still get the majority of our methane from natural gas, a fossil fuel, often from fracking, the ability to generate methane from a renewable hydrogen source is another important advance.” Adds Yang, “While we were inspired by the process of natural photosynthesis and continue to learn from it, by adding nanotechnology to help improve the efficiency of natural systems we are showing that sometimes we can do even better than nature.”
Schematic illustration of single molecule-junctions consisting stacks of aromatic molecules in a self-assembled cage and the corresponding electronic components of the junctions. The assembled cage is sandwiched by two Au electrodes. Empty cage (a), homo-stacks and hetero-stacked pair (c) develop functions of resistor, wire and diode, respectively. (click on image to enlarge) The empty cage presents a low electronic conductance (10